Abstract

Background

The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale
genome sequencing projects. The existence of this data offers scientists the possibility
of discovering additional genomic sequences beyond those originally sequenced. In
particular, if the source DNA for a sequencing project came from a species that was
colonized by another organism, then the project may yield substantial amounts of genomic
DNA, including near-complete genomes, from the symbiotic or parasitic organism.

Results

By searching the publicly available repository of DNA sequencing trace data, we discovered
three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three
new species, the data recovered were sufficient to produce an assembly that covers
more than 95% of the genome; for a second species the data produce the equivalent
of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome;
and for the third species the data cover approximately 6-7% of the genome.

Conclusions

The results of this study reveal an unexpected benefit of depositing raw data in a
central genome sequence repository: new species can be discovered within this data.
The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions
within each lineage and hundreds of novel genes. The three new genomes, with annotation,
have been deposited in GenBank.